So, i'm using 'orient' to get the principal axis of inertia (long axis) for
an alpha-helix, using this script.....Well, its 2 short regions on the same
helix -HHHHHH--HHHHH 'proximal' and 'distal' respectively

cd ~/Desktop/Doctorate/A/A1/proximal

lappend auto_path ../../../../scripts/la1.0

lappend auto_path ../../../../scripts/orient

package require Orient

namespace import Orient::orient

set nf [molinfo top get numframes]

set outfile [open 0to2.dat w]

set del [atomselect top "index 37 to 59"]

for { set i 1 } { $i < $nf+1 } { incr i } {

$del frame $i

set J [draw principalaxes $del]

puts $outfile "[lindex $J 2]"

}

close $outfile

cd ../distal

set outfile [open 0to2.dat w]

set del [atomselect top "index 60 to 73"]

for { set i 1 } { $i < $nf+1 } { incr i } {

$del frame $i

set J [draw principalaxes $del]

puts $outfile "[lindex $J 2]"

}

close $outfile

The script outputs 2 vectors for evey timestep and i get the angle by
180-cos(a.b) in the usual way. These vectors correspond to the least
eigenvalue of the problem,